diff searchgui.xml @ 22:e3be595c0bf5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
author iracooke
date Fri, 07 Aug 2015 06:55:04 -0400
parents dfaea053e32f
children 913dbf2b83e0
line wrap: on
line diff
--- a/searchgui.xml	Tue Jun 16 23:43:39 2015 -0400
+++ b/searchgui.xml	Fri Aug 07 06:55:04 2015 -0400
@@ -20,6 +20,10 @@
         mkdir output;
         mkdir output_reports;
         cwd=`pwd`;
+
+        cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
+        tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
+
         #for $mgf in $peak_lists:
             #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
             ln -s -f '${mgf}' '${input_name}';
@@ -32,7 +36,7 @@
         ###########################################
         #if $create_decoy:
             echo "Creating decoy database.";
-            java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
+            java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
             rm input_database.fasta &&
             cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
             ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
@@ -42,7 +46,7 @@
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
 
-        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
+        (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
             -out SEARCHGUI_IdentificationParameters.parameters
 
             @GENERAL_PARAMETERS@
@@ -247,7 +251,7 @@
         ################
         ## Search CLI ##
         ################
-        (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 
+        (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI 
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output